• Create a new Perk in the Creation Kit.
• Make sure the Perk has Playable checked. This is what tells the game to show the perk in the Level Up Menu, when the player levels.
• If you want to show the Perk as a Trait, make sure that both Playable and Trait are checked.
• All perks with custom Perk swf files need to have the swf path set on the perk. The automatic filename for perks includes the Load Order FormID of the perk, so if your plugin file isn't loaded in the same slot by the user as you develop it for, it won't work.
• If the perk has multiple ranks, make sure that only the first rank has the swf path set or that the perks have different levels. the same swf file will be shown for all ranks of a perk, but again, only the first rank should have the swf path. If you give the perk a sound, again, only the first rank can be set.
• Check the log to ensure your perk rank chains are set up correctly. If they are not, the incorrectly setup perk chain will have
  its members displayed in <My Games/Fallout 4/F4SE/ProjectMassachusetts.log>.
  

Supported Conditions:

• GetValue, which you probably don't want to use, since skill checks can be bypassed with chems and magazines.
• GetPermenantValue, which you probably want to use, which checks the base value of the skill + any permenant modifiers.
• GetBaseValue, which you probably don't want to use, since it won't account for any points added to a skill from tagging it, leveling up, or other perks that affect skills.
• GetGlobalValue, which is not displayed to the user, and hides the perk from the menu if the comparison fails
• GetIsSex, which also is not displayed, and also removes the perk from the menu if it fails (only GetIsSex == is supported).
• HasPerk, which only supports == and !=. If != fails, then the perk is removed from the menu. == checks are displayed.
  

If you need a different condition supported, or these support methods changed, tell me, and I'll work on it. These 4 are all I needed to implement all of the New Vegas perks. All checks are currently only done against the player, there is no support for checking the actor value of a companion or something.